Shepard has been exposed to Repear technology time and time again. First Eden Prime, then Virmire,the Prothean Cipher, boarding a derelict Reaper, engaging with Repear made enemies(Collectors) on their Repear made space station, fighting a human Repear, gathering Prothean and Collector technology, all of which could have residual Repear indoctornation powers to them AND not to mention, actually being in the presence of Repears and fighting them and their hordes. Oh and let's not forget Cerburus and the potential of them having been using Repear technology from day one.
Since Repears can be defeated with weapons, their real road to victory is through indoctornation. Throughtout the ME games, not one indoctirnated person has ever really snapped out of it and resumed their lives. But individual Repears can be destroyed...it's difficult, but they can be defeated through convential weapons.
IF your Shepard wakes up after the whole "choose the future, relays explode" scene, THAT is the good ending. That means that he was able to resist complete indoctirnation and is still in the fight. This is a good ending because it suggests that since the Repears failed to break him, and he can continue the fight.(How you get this ending is a topic for another post)
It's kind of like the Starship Troopers ending. It doesn't show a victory for the human race but shows that there is hope and that they will keep fighting.